This core functionality can be extended by adding one or more toolboxes. These are optional collections of tools for specific tasks, such as Mascot search result review, automatic and manual de novo sequencing, and batch processing. There is also a developer’s package that provides access to the API of the underlying COM library.

How it Works

Mascot Distiller detects peaks by attempting to fit an ideal isotopic distribution to the experimental data. This ideal distribution is predicted from the elemental composition expected for a peptide of average amino acid composition at that point on the mass scale. The profile of the ideal distribution is then adjusted by varying the mass, resolution, intensity, and charge state, so as to maximise the correlation with the experimental data. Once the best fit has been obtained, the peak is added to the peak list and the corresponding signal subtracted from the spectrum. The process is repeated until all the significant peaks have been fitted.

The advantage of this approach over conventional peak detection is that the complete experimental isotopic distribution is fitted, not just the 12C peak. The charge state is automatically determined and the peak list contains only monoisotopic peaks, even when the signal to noise is poor or the isotopic distribution not fully resolved. Smoothing is not necessary or desirable.

Cross-platform data browser

Mascot Distiller supports all the following data file formats:

Agilent

DataAnalysis (yep) (LC/MS Trap)

MassHunter (Q-TOF)

AB Sciex

Analyst (QStar, QTrap)

Data Explorer (Voyager*, 4700, 4800)

Bruker

Data/Flex Analysis (yep) (Esquire)

Data/Flex Analysis (baf) (Apex, MicrOTOF)

XMASS/XTOF (Reflex, Biflex, etc.)

Shimadzu

Kompact (Axima)

LCMSSolution (LCMS-IT-TOF)*

Thermo

Xcalibur (LCQ, LTQ, Orbitrap)

Waters

MassLynx (QTof, M@ldi, TofSpec, Synapt)

mzXML 2.0 and 2.1 (XML interchange format)

mzML 1.1 (XML interchange format)

Text (ASCII mass and intensity values)

* For these formats, Mascot Distiller requires access to library files (DLL’s or OCX’s) supplied as part of the corresponding instrument data system. All trade marks and service marks on this page are the properties of their respective owners and are hereby acknowledged.

Optimised Peak Detection

The main problems with conventional peak-picking algorithms are:

Failure to pick low intensity peaks

Picking peaks that are just noise

Selection of the wrong peak(s) or all peaks in an isotopic cluster

Need to continually “tweak” parameters

The algorithm used in Mascot Distiller addresses all of these problems by fitting the complete isotope distribution, then applying two thresholds to the peak list – signal/noise ratio and correlation coefficient. The result is peak detection, not noise detection:

Peak lists can be viewed, sorted, edited and saved to MGF and DTA format files, as well as a comprehensive format that includes additional information for each peak. Peak lists can be submitted direct to a Mascot server for database searching. The entire Mascot Distiller workspace, including peak lists and preferences, can be saved to a project file.

Mascot Distiller core functionality can be expanded using optional Toolboxes.